Anab initio theoretical study of the binding of ZnII with biologically significant ligands: CO2, H2O, OH−, imidazole, and imidazolate

Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential

As the second most abundant cation in human body, zinc is vital for the structures and functions of many proteins. Zinc-containing matrix metalloproteinases (MMPs) have been widely investigated as potential drug targets in a range of diseases ranging from cardiovascular disorders to cancers. However, it remains a challenge in theoretical studies to treat zinc in proteins with classical mechanics. In this study, we examined Zn(2+) coordination with organic compounds and protein side chains using a polarizable atomic multipole based electrostatic model. We find that polarization effect plays a determining role in Zn(2+) coordination geometry in both matrix metalloproteinase (MMP) complexes and in zinc-finger proteins. In addition, the relative binding free energies of selected inhibitors binding with MMP13 have been estimated and compared with experimental results. While not directly interacting with the small molecule inhibitors, the permanent and polarizing field of Zn(2+) exerts a strong influence on the relative affinities of the ligands. The simulation results also reveal the polarization effect on binding is ligand dependent and thus difficult to be incorporated into fixed-charge models implicitly.

Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for zinc complexes

A set of 44 Zinc-ligand bond-lengths and of 60 ligand-metal-ligand bond angles from 10 diverse transition-metal complexes, representative of the coordination spheres of typical biological Zn systems, were used to evaluate the performance of a total of 18 commonly available density functionals in geometry determination. Five different basis sets were considered for each density functional, namely two all-electron basis sets (a double-zeta and triple-zeta formulation) and three basis sets including popular types of effective-core potentials: Los Alamos, Steven-Basch-Krauss, and Stuttgart-Dresden. The results show that there are presently several better alternatives to the popular B3LYP density functional for the determination of Zn-ligand bond-lengths and angles. BB1K, MPWB1K, MPW1K, B97-2 and TPSS are suggested as the strongest alternatives for this effect presently available in most computational chemistry software packages. In addition, the results show that the use of effective-core potentials (in particular Stuttgart-Dresden) has a very limited impact, in terms of accuracy, in the determination of metal-ligand bond-lengths and angles in Zinc-complexes, and is a good and safe alternative to the use of an all-electron basis set such as 6-31G(d) or 6-311G(d,p).

Quantum mechanical/molecular mechanical and density functional theory studies of a prototypical zinc peptidase (carboxypeptidase A) suggest a general acid-general base mechanism

Carboxypeptidase A is a zinc-containing enzyme that cleaves the C-terminal residue in a polypeptide substrate. Despite much experimental work, there is still a significant controversy concerning its catalytic mechanism. In this study, the carboxypeptidase A-catalyzed hydrolysis of the hippuryl-L-Phe molecule (k(cat) = 17.7 +/- 0.7 s(-1)) is investigated using both density functional theory and a hybrid quantum mechanical/molecular mechanical approach. The enzymatic reaction was found to proceed via a promoted-water pathway with Glu270 serving as the general base and general acid. Free-energy calculations indicate that the first nucleophilic addition step is rate-limiting, with a barrier of 17.9 kcal/mol. Besides activating the zinc-bound water nucleophile, the zinc cofactor also serves as an electrophilic catalyst that stabilizes the substrate carbonyl oxygen during the formation of the tetrahedral intermediate. In the Michaelis complex, Arg127, rather than Zn(II), is responsible for the polarization of the substrate carbonyl and it also serves as the oxyanion hole. As a result, its mutation leads to a higher free-energy barrier, in agreement with experimental observations.

Comparative assessment of theoretical methods for the determination of geometrical properties in biological zinc complexes

In the present study, we have compared the performance of the density functional theory (DFT) functionals B1B95, B3LYP, B97-2, BP86, and BPW91 with MP2 for geometry determination in biological mononuclear Zn complexes. A total of 15 different basis sets, of rather diverse complexity, were tested, several which included also three different types of common effective-core potentials: Los Alamos, Steven-Basch-Krauss, and Stuttgart-Dresden. In addition, the ability to describe mononuclear Zn biological systems using relatively simple models of the metal coordination sphere, comprising only the metal atom and a simplified representation of the ligands at the first coordination sphere, starting from a set of high-resolution X-ray crystallographic structures, is evaluated for 90 combinations of method/basis set. The results show that the use of such models allows for a relatively accurate description of the Zn-ligand bond lengths, although failing to correctly represent the topology of the metal coordination sphere (namely, the angles involving the metal atom) if constraints at the Calpha atoms are not considered. Globally, B3LYP had the best average performance in the test, closely followed by MP2, whereas B1B95 was the least accurate method. The study also points out B3LYP/CEP-121G and B3LYP/SDD, which use, respectively, the Steven-Basch-Krauss and the Stuttgart-Dresden effective-core potentials, as the best compromise between accuracy and CPU time for the geometrical characterization of metal-ligand bond lengths in Zn biological systems.

Cs(2) fixation by carbonic anhydrase model systems-a new substrate in the catalytic cycle

The conversion of CS(2) with common carbonic anhydrase model systems has been studied using Hartree-Fock and density-functional theory methods employing the 6-311+G basis set. The calculated geometries and energetical parameters for [L(3)ZnOH](+)/CS(2) model systems (L = NH(3), imidazole) are compared with those obtained previously for the CO(2) hydration. While the same reaction mechanism applies for both heterocumulenes, the hypothetical conversion of CS(2) to give [L(3)ZnSC(O)SH](+) is characterized by a higher barrier and is much more exothermic than the corresponding CO(2) reaction cascade. Due to the increased number of heteroatoms, additional intermediates and product structures (compared with those involved in the CO(2) conversion) must be taken into account and have been analyzed in detail. The smaller electrophilicity of CS(2) is the reason for the higher activation energies, while the significantly increased exothermicity is due to the strong zinc(II)/sulfur interaction. The reversibility and therefore the existence of a catalytic cycle which could allow comparable CS(2) transformations must be questioned. Nevertheless, an interesting field of stoichiometric zinc-mediated CS(2) transformations is conceivable.

Zinc binding in proteins and solution: a simple but accurate nonbonded representation

Force field parameters that use a combination of Lennard-Jones and electrostatic interactions are developed for divalent zinc and tested in solution and protein simulations. It is shown that the parameter set gives free energies of solution in good agreement with experiment. Molecular dynamics simulations of carboxypeptidase A and carbonic anhydrase are performed with these zinc parameters and the CHARMM 22 beta all-atom parameter set. The structural results are as accurate as those obtained in published simulations that use specifically bonded models for the zinc ion and the AMBER force field. The inclusion of longer-range electrostatic interactions by use of the Extended Electrostatics model is found to improve the equilibrium conformation of the active site It is concluded that the present parameter set, which permits different coordination geometries and ligand exchange for the zinc ion, can be employed effectively for both solution and protein simulations of zinc-containing systems.

Theoretical study of oxyhemocyanin active site: a possible insight on the first step of phenol oxidation by tyrosinase

Extended Huckel theory calculations have been carried out on a model of the oxyhemocyanin active site that includes six imidazoles, the two copper cations, and a dioxygen molecule. The results obtained for the very likely mu-eta 2:eta 2 arrangement of the dioxygen molecule show that the most favorable orientation of O2 is such that the two long Cu-N coordination bonds are perpendicular to the plane formed by the two metal atoms and O2. This arrangement leads to pentacoordinated coppers with a distorted square pyramidal geometry. The molecular electrostatic potential maps of the complexes exhibit a potential well located close to the peroxo anion midbond. The dependence of the energy and of the molecular electrostatic maps on the precise orientation and location of the imidazole rings has been investigated. These results, which show the important role played by the third remote imidazole ligand, are discussed in relation with the first step of tyrosinase-mediated phenol oxidation.

A theoretical study of Zn++ interacting with models of ligands present at the thermolysin active site

The binding energy and the geometrical arrangements of the complexes formed by the zinc dication with OH-, one, four, five or six water molecules, SH-, H2S, formic acid, the formate anion, imidazole, its anion and formamide are calculated using the MNDO method. The comparison of the results obtained with those of ab initio computations on the same complexes induced us to propose for Zn++ a set of parameters different from the one determined by Dewar for the neutral metal atom. Using the two MNDO parametrizations, similar calculations are carried out for Zn++ interacting with two molecules of 2-aminoethanethiol and with models of the four ligands which are present at the thermolysin active site, in order to evaluate the possibilities and limitations of this semiempirical method for theoretical studies concerning zinc metalloenzymes. In the last case, the results obtained suggest that, in the crystal state, the water molecule could be deprotonated. This finding is discussed in relation with the mechanism of action of the enzyme which has been proposed.